|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectowltools.panther.PANTHERTree
public class PANTHERTree
Methods to simplify the work with the Newick-ish output we get from PANTHER.
Constructor Summary | |
---|---|
PANTHERTree(File pFile)
Create an instance for the given path |
Method Summary | |
---|---|
Set<String> |
associatedIdentifierSet()
Return a set of all identifiers associated with this family. |
Set<String> |
getAncestorAnnotations(String baseGpID)
Return all annotations to ancestor nodes. |
Set<String> |
getAncestors(String nodeID)
Return the ancestors of this node as an ID set. |
Set<String> |
getDescendantAnnotations(String baseGpID)
Return all annotations to descendant nodes. |
Set<String> |
getDescendants(String nodeID)
Return the descendants of this node as an ID set. |
String |
getNHXString()
Return the raw Newick-type input string. |
OWLShuntGraph |
getOWLShuntGraph()
Return the complete OWL shunt graph repesentation of the phylogenic tree. |
String |
getTreeID()
Return the tree identifier. |
String |
getTreeLabel()
Return the tree label. |
String |
setTreeLabel(String lbl)
Set the tree label. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public PANTHERTree(File pFile) throws IOException
path
-
IOException
Method Detail |
---|
public String getNHXString()
public String getTreeLabel()
public String setTreeLabel(String lbl)
public String getTreeID()
public OWLShuntGraph getOWLShuntGraph()
public Set<String> getAncestors(String nodeID)
node
- id
public Set<String> getDescendants(String nodeID)
node
- id
public Set<String> getAncestorAnnotations(String baseGpID)
gene
- product id
public Set<String> getDescendantAnnotations(String baseGpID)
gene
- product id
public Set<String> associatedIdentifierSet()
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |